This invention is in the general area of genetic engineering of nucleic acid sequences, especially chemically modified external guide sequences and catalytic RNA sequences linked to guide sequences.
There are several classes of ribozymes now known which are involved in the cleavage and/or ligation of RNA chains. A ribozyme is defined as an enzyme which is made of RNA, most of which work on RNA substrates. Ribozymes have been known since 1982, when Cech and colleagues (Cell 31: 147-157) showed that a ribosomal RNA precursor in Tetrahymena, a unicellular eukaryote, undergoes cleavage catalyzed by elements in the RNA sequence to be removed during the conversion of the rRNA precursor into mature rRNA. Another class of ribozyme, discovered in 1983, was the first to be shown to work in trans, that is, to work under conditions where the ribozyme is built into one RNA chain while the substrate to be cleaved is a second, separate RNA chain. This ribozyme, called M1 RNA, was characterized in 1983 by Altman and colleagues as responsible for the cleavage which forms mature 5' ends of all transfer RNAs (tRNAs) in E. coli. Analogous RNA-containing enzymes concerned with tRNA synthesis have since been found in all cells in which they have been sought, including a number of human cell lines, though the relevant eukaryotic RNAs have not yet been shown to be catalytic by themselves in vitro.
The discovery and characterization of this catalytic RNA is reviewed by Sidney Altman, in "Ribonuclease P: An Enzyme with a Catalytic RNA Subunit" in Adv. Enzymol. 62: 1-36 (1989). The activity was first isolated from E. coli extracts, and subsequently determined to be a ribonucleoprotein having two components, an RNA component called M1 and a protein component called C5. The RNA cleaved substrates in a true enzymatic reaction, as measured using Michaelis-Menten kinetics. M1 was determined to be solely responsible for substrate recognition and C5 was determined to alter k.sub.cat but not K.sub.M, as reported by Guerrier-Takada et al., Cell 35: 849 (1983) and McClain et al., Science 238: 527 (1987). Sequencing showed that M1 RNA is 377 nucleotides long, M.sub.r approximately 125,000, and that the protein consists of 119 amino acids, M.sub.r approximately 13,800, as reported by Hansen et al., Gene 38: 535 (1987).
Cleavage of precursor tRNA molecules by the RNA component of eubacterial RNase P is described by Guerrier-Takada et al., Cell 35, 849 (1983) and reviewed by Altman, Adv. Enzymol. 62:1 (1989).
U.S. Pat. No. 5,168,053 entitled "Cleavage Of Targeted RNA By RNase P" to Altman et al., discloses that it is possible to target any RNA molecule for cleavage by bacterial RNase P by forming a nucleotide sequence part of which is complementary to a targeted site and which includes a terminal 3'-NCCA, wherein the sequence is designed to hybridize to the targeted RNA so that the bacterial RNase P cleaves the substrate at the hybrid base-paired region. Specificity is determined by the complementary sequence. The sequence is preferably ten to fifteen nucleotides in length and may contain non-complementary nucleotides to the extent this does not interfere with formation of several base pairs by the complementary sequence which is followed by NCCA at the 3' end.
As described in WO 92/03566 to Yale University, ribonuclease P (RNase P) from E. coli can cleave oligoribonucleotides that are found in hydrogen-bonded complexes that resemble the aminoacyl stem and include the 5' leader sequence of tRNA precursors, --NCAA. Human RNase P cannot cleave in vitro the 5' proximal oligoribonucleotide in the simple complexes cleaved by RNase P from E. coli, but can do so when the 3' proximal oligoribonucleotide is bound to an external guide sequence (EGS) to form a structure resembling portions of a tRNA molecule. The EGS can include a complementary sequence to a target substrate of at least eleven nucleotides, seven bases which hydrogen bond to the targeted sequence to form a structure akin to the aminoacyl acceptor stem of a precursor tRNA, and four nucleotides which base pair with the targeted sequence to form a structure akin to the dihydroxyuracil stem. WO 92/03566 does not disclose EGS for prokaryotic RNase P with fewer than seven complementary nucleotides.
WO 93/22434 to Yale University discloses an EGS for human RNase P. As described in WO 93/22434, an EGS for human RNase P consists of a sequence which, when in a complex with the target substrate molecule, forms a secondary structure resembling that of a tRNA cloverleaf, or a substantial part of it, and that results in cleavage of the 10 target RNA by RNase P. The sequence of the EGS of WO 93/22434 is derived from any tRNA except that the D stem and aminoacyl stem are altered to be complementary to the target substrate sequence. WO 93/22434 also discloses EGS with either the anticodon loop and stem or the extra loop deleted, and EGS where the sequence of the T loop and stem are changed. WO 93/22434 does not disclose eukaryotic EGS comprising only a region complementary to the target RNA and a region forming a structure similar to only the T stem and loop of tRNA. Neither WO 92/03566 nor WO 93/22434 discloses EGS having chemically modified nucleotides.
It is therefore an object of the present invention to provide methods and compositions for specifically cleaving targeted RNA sequences using linked catalytic RNA and minimal guide sequences.
It is another object of the present invention to provide chemically modified external guide sequences for RNase P with enhanced resistance to nuclease degradation.
It is another object of the present invention to provide a method for selecting external guide sequences, and linked catalytic RNA and guide sequences, that cleave a target RNA with increased efficiency.
It is a further object of the present invention to provide methods and compositions for specifically cleaving RNA, both in vitro and in vivo within eukaryotic cells, for the treatment of disease conditions which involve RNA transcription or translation, such as diseases caused by RNA and DNA viruses and expression of excessive or pathogenic proteins from mRNA, or of excessive or pathogenic RNA, itself.